1 research outputs found
On the propensity of Asn-Gly-containing heptapeptides to form -turn structures : comparison between ab initio quantum mechanical calculations and Molecular Dynamics simulations
Both molecular mechanical and quantum mechanical calculations play an
important role in describing the behavior and structure of molecules. In this
work, we compare for the same peptide systems the results obtained from folding
molecular dynamics simulations with previously reported results from quantum
mechanical calculations. More specifically, three molecular dynamics
simulations of 5 s each in explicit water solvent were carried out for
three Asn-Gly-containing heptapeptides, in order to study their folding and
dynamics. Previous data, based on quantum mechanical calculations and the DFT
methods have shown that these peptides adopt -turn structures in aqueous
solution, with type I' -turn being the most preferred motif. The results
from our analyses indicate that for the given system the two methods diverge in
their predictions. The possibility of a force field-dependent deficiency is
examined as a possible source of the observed discrepancy.Comment: In the supplementary information file figures S5, S6 and S7 the
-turn occupancies were wrong. They have been correcte